4QI2 | pdb_00004qi2

X-ray structure of the ROQ domain from murine Roquin-1 in complex with a 23-mer Tnf-CDE RNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4QI0	pdb entry 4QI0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	200 mM NaCl, 100 mM Bis-Tris, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.56	α = 105.68
b = 60.41	β = 101.36
c = 84.37	γ = 95.72

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2014-01-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.03321	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	3	50	95.7	0.07	13.9		19951	19951

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.08	96.9		0.513	3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 4QI0	3	50	18931	18931	1020	95.82	0.20549	0.20316	0.2092	0.24679	0.2473	RANDOM	77.711

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
6.29	6.88	-1.27	-5.25	0.73	-1.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.798
r_dihedral_angle_3_deg	18.243
r_dihedral_angle_4_deg	13.619
r_long_range_B_other	13.417
r_long_range_B_refined	13.416
r_scangle_other	9.992
r_mcangle_it	8.88
r_mcangle_other	8.879
r_scbond_it	6.637
r_scbond_other	6.633
r_mcbond_it	5.921
r_mcbond_other	5.908
r_dihedral_angle_1_deg	5.589
r_angle_refined_deg	1.513
r_angle_other_deg	1.166
r_chiral_restr	0.075
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_gen_planes_other	0.006
r_bond_other_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4895
Nucleic Acid Atoms	1576
Solvent Atoms	32
Heterogen Atoms

Software

Software
Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling